The use of high-resolution continuum-source graphite furnace atomic absorption spectrometry (HR-CS GF AAS), equipped with a linear charge-coupled device (CCD) array detector, makes simultaneous determination of more than one element possible. In this work, HR-CS GF AAS was used for the simultaneous determination of Mo (313.259 nm) and Ni (313.410 nm), for which two analytical methods were developed: direct solid sample analysis for soil amendments and direct sample injection for wine samples. For both these methods, a pyrolysis temperature of 1200 °C and an atomization temperature of 2650 °C were used. Aqueous standard solutions were used for calibration. The linear correlation coefficient was higher than 0.997 for the two analytes. Detection limits of 0.05 and 0.8 μg L−1 for wine samples and 0.04 and 0.60 mg kg−1 for soil amendments were found for Mo and Ni, respectively. To investigate the accuracy of the developed method, digested and undigested wine samples were evaluated with spike recovery values between 94% and 106%. For solid samples, three CRM were evaluated, and the values found for Mo were not significantly different from the certified ones; however, those for Ni were always too high. It was found that this was due to a direct line overlap of the Ni line with the Fe line. This effect was overcome by determining Fe using the unresolved analytical line doublet at 312.565/312.568 nm and subtracting this value from the total concentration (Ni + Fe) determined at 313.410 nm. Note that this interference was not observed in wine samples because of their low Fe concentration.